added tests for find_pairs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1987 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/find_pairs.in b/bp_test/in/find_pairs.in
new file mode 100644 (file)
index 0000000..f9a2a66
--- /dev/null
+++ b/bp_test/in/find_pairs.in
@@ -0,0 +1,140 @@
+SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB
+SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NNNNNGNNNNNNNTANACNNNNTNNNNNNNANNNNGNNNNNCNNNNNGNN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NNNNNNNNGGNNCNANNANNNNGTNNNTNGNANNNNCNNANTTGNNNNNN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1041:14486#TTAGGC/2
+---
+SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB
+SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1
+---
+SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2
+---
+SCORES: ffffcfffffded^eddddddbdcdeedcefecfefdffecabccBB`b`
+SEQ: CCNAGGAGGAGNCAATAAGAGACCATTCGTATATGATCTCTCAGGAGAGC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1044:7943#TTAGGC/1
+---
+SCORES: ceceeee\e``cd^^Yb`b`cc``c\accccZT`YTbYb`Y\VZYBBa\Y
+SEQ: GCCGAGTAGCGTTCNTGGNTACCTTCCGATCCGCGGCCCGCCCCCTGTCT
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1
+---
+SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+SEQ: AANAANANCTNCNNANCGNCGGTTTCGTNANNANNGGTTCGCANCGNNNC
+SEQ_LEN: 50
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 2:N:0:TAGCTG
+SEQ: CTACCTGTGCAAAAAGCACCAAGCAGAGCCATGCTNAACATGGACAGGCGAGCTGGTGTCATAAACATTTCCTGNTTTTANTCTATNGTAGNTANTAA
+SEQ_LEN: 98
+SCORES: bbbeeeecggfeghfggfhihhieh]ffbeghiiiBOYcfghighfghghaedfeeV^abcccce`bdbdc```BKZ^aaBKW^^aBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 2:N:0:TAGCTG
+SEQ: CCGGGCTTGATGCCCTGGCATTGGAGCAATACGAGTTGTTGCTGGAAGAACAAGCCTATCCGTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
+SEQ_LEN: 98
+SCORES: ^^_eee^ccgeggiidfdd_ggfhhhfhifhhfgfggffgdeghe_ebfgedfXZcffdggdT`^aeeee^`bcacc\^Z^a[]Q[`b^]^aaBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 2:N:0:TAGCTG
+SEQ: CCATCACGCAATCTGCTAACACCGACAGATAACGCTCGCGCCAACGCAGATCTGTATTGCGGGCATCCTGCATATTACTGTTAGGAATAGATCGGAAG
+SEQ_LEN: 98
+SCORES: ZZac^cd`gf`eeifhh`dfbaafagha`g`_`e`a^cZ`edS\deedcc`^_]]bccRTZQW[T^bbb__bbbb__bc]bc_R^bc]_]bbba[[^R
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 1:N:0:TAGCTG
+SEQ: CATAGGCTTTTTTAACGGCCCAGCCAAAGGCGATCAGGCCAAATAGNANTACCCACCAGTACTGTTGCATNGTCTCAGAAATGNNCAATACAAATTGG
+SEQ_LEN: 98
+SCORES: _[_cccccgcaeeaeJb`b^dd_cg]cZedbfU_eghhhddfg[f]BLBLTZ^abbb^aT]b_`]`b`Y`BKT^^ac_YYY_`BBJGQW_b]bbbbbb
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 1:N:0:TAGCTG
+SEQ: GCTTTGACATAGTCGCTCCAGAATTGCCAGCTAGGGTTAGCTTGGCAACTGCAGCGACGTAATGTGCTGTGGCAGATCAATTTATCTGTTTTGAATCA
+SEQ_LEN: 98
+SCORES: ^P^PJ\Y`eea`e[daYdecggadgdXJIYVbdc`efg_cdedI^aXIO^abeb\eL_daQU^_V]``]UGTZ\^BBBBBBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 2:N:0:TAGCTG
+SEQ: AACAAACTGTTTTGCAGAATGTTATGAATGGTCCGNGCGCNTNAACCCAGATCGGAAGAGCGTCGTGTAGGGAANGANGGNNGNNCNCGGNNNNNGNC
+SEQ_LEN: 98
+SCORES: a__eeecegcgegihhifhhfcgdghfffiibgheBPPYcBOBOXaffffgfhhhffa`bfe\^cR]Z]`baZ`BBBBBBBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 1:N:0:TAGCTG
+SEQ: CTGGGTGCCACTGTCGCCACCCTGTTAAGTCGTGAACCCGTTACCATCAGCACTGATGCCAACGTCTGGCAGGCCGCCCAGCTAATGACCGAGCAAAA
+SEQ_LEN: 98
+SCORES: _[_cccceeegggffhiiihdfdefhhafeff_efdfgfhifhghhfbgbgdggfdhihhegggeeeebdZ^aaa^_aaX``b]b_bcccXXaV_ccb
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 1:N:0:TAGCTG
+SEQ: CGCCTTTTCATCAGCAACAGACAGTTACGACGCATATCGCCACCCAAATGTTTGCCGAGGCTAAACGGGTATTGAAACGCGGTGGCCGCTTGCGTATT
+SEQ_LEN: 98
+SCORES: ___eeeeegagffgghdefb_e_eggia`\egfdhhdf`gdfghihiiib_`gghf``cbcabcbc^^_KW`c]Y_bbcc[a[[_^aa]cccc]__ab
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 1:N:0:TAGCTG
+SEQ: AAACGGATAGGCTTGTTCTTCCAGCAACAACTCGTATTGCTCCAATGCCAGGGCATCAAGCCCGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+SEQ_LEN: 98
+SCORES: _bbaceceggeccgeZddghaegffiiWdghfff``ffgfacfcffhiihhfi\_e\egfcggde]acdccc^aa_`[`aca_a^b_`bbbbbbbS_b
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 2:N:0:TAGCTG
+SEQ: GGCCAAATAACCGCTGCAGTTGCTGCTGATAATTCAGGTGACGGTTAGCCACAATACGCAAGCGGCCACCGCGTTTCAATACCCGTTTAGCCTCGGCA
+SEQ_LEN: 98
+SCORES: bbbeeeeegfgggiehihhef_gfgfhfghdffhihhfXc^egc_cgabgffghhfhfhfg`d^cba_ac^\_W]abcb_bccc]X`bQ]`b`^_a__
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 2:N:0:TAGCTG
+SEQ: AGCCTGGCCCGGATATCCTTGTCAGTGATAATGCCNGTCAGATGCTGCTTGGCATCTAAAATAAGCAAGGATGANACCTTNTGNTCNGTCNNTANCTG
+SEQ_LEN: 98
+SCORES: b__eeeeeggggcgghiiiihefggcgeffagdbfBOY^cffhfgbgfhdggXegghagghfffeggggeXV^_BKZ\_cBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 1:N:0:TAGCTG
+SEQ: TACCTAAAATAATTAATATCTACAATAGAATAAAATCAGGAAATGTTTATGACACCAGCTCGCCTGTCCATGTTCAGCATGGCTCTGCTTGGTGCTTT
+SEQ_LEN: 98
+SCORES: __acceeegcgggiihihifiiiiiiiiiiefihhhhchhdhiafcghidffghhiihidfggighedhdhibdggegdgeeeedddcddccbcccab
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 1:N:0:TAGCTG
+SEQ: GGGTTCAGGCGCCCGGACCATTCATAACATTCTGCAAAACAGTTTGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTGATCTCGTATG
+SEQ_LEN: 98
+SCORES: ___J`cccgZccggghhhhffhbghhfeegffdghhfchhhfaffgbb]e`_c\a_\degdddbbb``^aY]bbb_bbbbbbb`bbbb_]`R]^[WR[
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 1:N:0:TAGCTG
+SEQ: GTGCCAAAGAGGTACTGATGCTTTGTTGTTGTGGTTTAGCCGCACATTCAGCCTCGCTGACGGCAGCTAACTGCACATCTTTGGGGATATCCACCAGA
+SEQ_LEN: 98
+SCORES: ^PWYP`R^cRcccgdghS`d_ebc[`ebffddb[ffffagf[O^_Uc`SabeffeegffW\\[XXR^bTGT__]b]_Y_]Zbbba][abb_cbba_aa
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 2:N:0:TAGCTG
+SEQ: GGTGGATATCCCCAAAGATGTGCAGTTAGCTGCCGNCAGCGAGGCTGAATGTGCGGCTAAACCACAACAACAAANCATCANTACCTNTTTGNCANAGA
+SEQ_LEN: 98
+SCORES: ___cc\c`eggcghad`acabgfdg`g^daagaefBPYOafY_fYaa]e\aMWW__[W^Z_RZ^`aa__`Q[`^BBBBBBBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 2:N:0:TAGCTG
+SEQ: ATGTGTCGATGCTGGATAACGAATGGGGTATGTCGGTGTATCCGCTGGGGGCTGGTCATGAAGGGGTGGGGCATATTGCAGCTGTGGGTTCGGGGGCC
+SEQ_LEN: 98
+SCORES: JJ\caa`^Ye`gW^[J[Q[`YJJ`dfa^PYbfX^^_H^^eh]fb`aefGZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 1:N:0:TAGCTG
+SEQ: CCACCTGCCCGGTTTTAAGATGACTGACCGCCGAACCCACAGCTGCAATATGCCCCACCACTTCATGACCAGCCACCAGCGGATACGCCGACATACCC
+SEQ_LEN: 98
+SCORES: _Z_cccccaY_^cghhbagg[e]de][^ZcghfY_efgfbfdQ^^\bdZaaRMZZT\FRT\LLYYZTGT]_[^a^[^aBBBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 1:N:0:TAGCTG
+SEQ: ATTCCTAACAGTAATATGCAGGATGCCCGCAATACAGATCTGCGTTGGCGCGAGCGTTATCTGTCGGTGTTAGCAGATTTCGTGATGGAGATCGGAAG
+SEQ_LEN: 98
+SCORES: ___cc`Sc^J[ecK``f]cY^RPbcRYJQQY^YccacfehhheU^^^eXFS_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 2:N:0:TAGCTG
+SEQ: CGGCCNNNACCCAATTTGNNTTGGGCATTTCTGANNNNNNNCNACNNTACTGNNGGGTANTGCTNNNTGNNNNGNNNNNNNNNNNNNNNNNNNNNNNN
+SEQ_LEN: 98
+SCORES: WZ^ceBBBQQQQbffgggBBSQ`_fRZdegffdhBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 2:N:0:TAGCTG
+SEQ: GGTTATCGATCTGGAAAAAGCAACTAAACCTAAAGCTAAACCACGTAGCGCCGGGTAAATGATTCAAAACAGATAAATTGATCTGCCACAGCACATTA
+SEQ_LEN: 98
+SCORES: ^VYPJQ`c^JJ[b[efg^dHJ`aa`adXd_ZXXbIIIY[af_H^aWHWPZ[`gggFFZ^bd_Z]Zb_]ba\^ZGY_`TZ``cc[bbR]]^aaXQ[bbb
+---

diff --git a/bp_test/out/find_pairs.out.1 b/bp_test/out/find_pairs.out.1
new file mode 100644 (file)
index 0000000..0611aa0
--- /dev/null
+++ b/bp_test/out/find_pairs.out.1
@@ -0,0 +1,52 @@
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1
+---
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2
+---
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1
+---
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2
+---
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1
+---
+SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 2:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 1:N:0:TAGCTG
+---
+SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 2:N:0:TAGCTG
+---

diff --git a/bp_test/test/test_find_pairs b/bp_test/test/test_find_pairs
new file mode 100755 (executable)
index 0000000..61c5709
--- /dev/null
+++ b/bp_test/test/test_find_pairs
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean